makePWMPvalCutoffBackgroundFromSeq {PWMEnrich}R Documentation

Construct a P-value cutoff background from a set of sequences

Description

This function creates a P-value cutoff background for motif enrichment.

Usage

  makePWMPvalCutoffBackgroundFromSeq(bg.seq, motifs,
    p.value = 0.001, bg.pseudo.count = 1, bg.source = "",
    verbose = TRUE)

Arguments

bg.seq

a set of background sequences, either a list of DNAString object or DNAStringSet object

motifs

a set of motifs, either a list of frequency matrices, or a list of PWM objects. If frequency matrices are given, the background distribution is fitted from bg.seq.

p.value

the P-value used to find cuttoffs for each of the motifs

bg.pseudo.count

the pseudo count which is shared between nucleotides when frequency matrices are given

bg.source

textual description of background source

verbose

if to print verbose output

Value

an object of type PWMCutoffBackground

Examples

## Not run: 
if(require("PWMEnrich.Dmelanogaster.background")){
   data(MotifDb.Dmel.PFM)

   # use the empirical background to pick a threshold and make cutoff background
   makePWMPvalCutoffBackground(Dmelanogaster$upstream2000, 0.001)
}

## End(Not run)
[Package PWMEnrich version 4.16.0 Index]